Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Ellie + Vader Talk
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Technical
Academic
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
fMRI Data is Noisy
fMRI = functional Magnetic Resonance Imaging
- Thermal
- Head Motion
- Spin History
- Heartbeat
- Heart Rate Variability
- Respiration
- Respiration Variability
- CO2 Variability
- Spontaneous Activity
- HRF Model Error
- Scanner instability
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Independent Components Analysis (Temporal)
True Sources
Observed Sources
ICA Sources
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Independent Components Analysis (Spatial)
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Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Example Time Series
(Left Motor)
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Independent Components Analysis (fMRI)
Spatial: 100,000+ data points
Time:
~100+ data points
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Automatic Removal of Motion Artifacts (AROMA)
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Signal & Noise Components
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Example Voxel Correlation
No Noise Removal
"Aggressive" Removal
"Non-Aggressive" Removal
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Review: ICA-AROMA
- Finds independent sources in data
- Identifies noise sources
- Is Aggressive or Non-Aggressive better?
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Code Contribution: ICA-AROMA
2017-05-02
2017-05-[03-10]
2017-05-26
-
2017-06-28
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
FMRIPrep: The Paper
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
FMRIPrep: My Next Contribution
- Currently - "Non-Aggressive" denoising THEN use other confounds
- Future - "Non-Aggressive" denoising SIMULTANEOUS with other confounds.
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
The Problem:
Modular Preprocessing
2018-02-02
2018-02-03
2018-04-11
2018-09-04
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
The Problem:
Modular Preprocessing
Favorite Drink?
Favorite Activity?
Favorite Treat?
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
The Problem:
Modular Preprocessing
Original Data
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
The Problem:
Modular Preprocessing
-
y' = ' y ~ confound1 '
- y_resid = y - y'
- y'' = ' y_resid ~ confound2 '
- y'_resid = y_resid - y''
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
The Problem:
Modular Preprocessing
-
y' = ' y ~ confound2 '
- y_resid = y - y'
- y'' = ' y_resid ~ confound1 '
- y'_resid = y_resid - y''
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
The Problem:
Modular Preprocessing
-
y' = ' y ~ confound1 + confound2'
- y_resid = y - y'
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Review:
Modular Preprocessing
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
- Don't Do Modular Preprocessing!
- Model everything you want to model
- Online Collaborations = Fun + Informative
Takeaways
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
- Understanding data is hard
- There are great communities online
- You can get recognized for your contributions
- Collaborations make science better!
Thanks!
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Dr. Chris Gorgolewski
&
Dr. Chris Markiewicz
HBC Lab
- Dr. Michelle Voss
- Matt Sodoma
- Adriana Rivera-Dompenciel
Thesis Committee
- Dr. Michelle Voss
- Dr. Jatin Vaidya
- Dr. Vince Magnotta
- Dr. Jan Wessel
- Dr. Eliot Hazeltine
Questions?
Slides: slides.com/jameskent/2018-seminar
Code: github.com/jdkent/2018-Seminar-Talk
Introduce myself and note the links to the slides and the code for the presentation
The Nuisance of Denoising fMRI James Kent ( @SudoNeuroSci ) Dr. Michelle Voss HBC Lab Slides: slides.com/jameskent/2018-seminar Code: github.com/jdkent/2018-Seminar-Talk
2018-seminar
By James Kent
2018-seminar
my 2018 seminar talk
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